Open the program and select Create patch. Under Original file browse to Alttp US No-header rom. Under Modified file browse to the Hack or any modified rom. Under Ups patch file to create type in the name of the patch (same as modified rom name), plus the .ups extension! That's it.

You have 2 options in applying the patch:The first one is: Apply patch to an existing file. In this case you just need to select the UPS patch and the target file. This file will be overwritten. Try to choose the US rom with header here. If the patch was made using US No-header, it will kindly remind you that the source file is invalid. The same if you use the EU rom. When the patching is successful, the resulting rom will be the exact rom, which the author used to make the patch.

The second option is to: Apply patch to a new file. Same as before, but instead of overwriting the file, a new file will be created. So you need to type the name of this file in the third field with the .smc extension!